Starting phenix.real_space_refine
on Sun Apr  5 17:04:55 2026 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/10ya_75522/04_2026/10ya_75522.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/10ya_75522/04_2026/10ya_75522.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/10ya_75522/04_2026/10ya_75522.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/10ya_75522/04_2026/10ya_75522.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/10ya_75522/04_2026/10ya_75522.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/10ya_75522/04_2026/10ya_75522.map"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     294      5.49       5
     S      10      5.16       5
     C    6625      2.51       5
     N    2250      2.21       5
     O    2819      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11998
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 800
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 641
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 641
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "C"
      Number of atoms: 832
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 832
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 725
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 725
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "E"
      Number of atoms: 800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 800
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 641
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 641
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 823
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 823
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "H"
      Number of atoms: 708
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 708
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 2, 'TRANS': 88}
    Chain: "I"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 1573
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 1573
          Classifications: {'DNA': 76}
          Link IDs: {'rna3p': 75}
    Chain: "K"
      Number of atoms: 1459
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 71, 1459
          Classifications: {'DNA': 71}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 70}
  Time building chain proxies: 2.69, per 1000 atoms: 0.22
  Number of scatterers: 11998
  At special positions: 0
  Unit cell: (74.328, 121.924, 122.576, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      10     16.00
     P     294     15.00
     O    2819      8.00
     N    2250      7.00
     C    6625      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.04
  Conformation dependent library (CDL) restraints added in 386.0 milliseconds
  

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1406

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 9 sheets defined
      73.4% alpha, 2.7% beta
      147 base pairs and 259 stacking pairs defined.
    Time for finding SS restraints: 1.81
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 49
    Processing helix  chain 'A' and resid 50 through 55
    Processing helix  chain 'A' and resid 63 through 76
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 131
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.629A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ARG B  55 " --> pdb=" O   TYR B  51 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
      removed outlier: 3.560A  pdb=" N   VAL C  30 " --> pdb=" O   PRO C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.358A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 104 through 123
      removed outlier: 3.502A  pdb=" N   LYS D 116 " --> pdb=" O   SER D 112 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 4.125A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 24 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.716A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.559A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.411A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
      removed outlier: 3.582A  pdb=" N   LYS G  95 " --> pdb=" O   GLU G  91 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 103 through 124
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.169A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.733A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.275A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.002A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.322A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78

    402 hydrogen bonds defined for protein.
    1182 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      376 hydrogen bonds
      752 hydrogen bond angles
      0 basepair planarities
      147 basepair parallelities
      259 stacking parallelities
  Total time for adding SS restraints: 2.15

  Time building geometry restraints manager: 1.40 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.33: 2323
        1.33 -     1.45: 4152
        1.45 -     1.57: 5730
        1.57 -     1.69: 585
        1.69 -     1.81: 20
  Bond restraints: 12810
  Sorted by residual:
  bond pdb=" N   ILE A  62 "
       pdb=" CA  ILE A  62 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.036 1.17e-02 7.31e+03 9.24e+00
  bond pdb=" N   TYR H  37 "
       pdb=" CA  TYR H  37 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.034 1.18e-02 7.18e+03 8.40e+00
  bond pdb=" N   ILE B  29 "
       pdb=" CA  ILE B  29 "
    ideal  model  delta    sigma   weight residual
    1.459  1.491 -0.032 1.25e-02 6.40e+03 6.42e+00
  bond pdb=" N   ASN H  63 "
       pdb=" CA  ASN H  63 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.027 1.19e-02 7.06e+03 5.23e+00
  bond pdb=" C   ILE A  62 "
       pdb=" O   ILE A  62 "
    ideal  model  delta    sigma   weight residual
    1.237  1.251 -0.015 1.07e-02 8.73e+03 1.90e+00
  ... (remaining 12805 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 18160
        1.85 -     3.69: 369
        3.69 -     5.54: 20
        5.54 -     7.39: 7
        7.39 -     9.24: 3
  Bond angle restraints: 18559
  Sorted by residual:
  angle pdb=" N   VAL A 117 "
        pdb=" CA  VAL A 117 "
        pdb=" C   VAL A 117 "
      ideal   model   delta    sigma   weight residual
     111.90  108.12    3.78 8.10e-01 1.52e+00 2.18e+01
  angle pdb=" CG  LYS H 108 "
        pdb=" CD  LYS H 108 "
        pdb=" CE  LYS H 108 "
      ideal   model   delta    sigma   weight residual
     111.30  118.36   -7.06 2.30e+00 1.89e-01 9.42e+00
  angle pdb=" N   ILE B  29 "
        pdb=" CA  ILE B  29 "
        pdb=" C   ILE B  29 "
      ideal   model   delta    sigma   weight residual
     109.34  102.97    6.37 2.08e+00 2.31e-01 9.37e+00
  angle pdb=" CG  LYS D 108 "
        pdb=" CD  LYS D 108 "
        pdb=" CE  LYS D 108 "
      ideal   model   delta    sigma   weight residual
     111.30  118.13   -6.83 2.30e+00 1.89e-01 8.83e+00
  angle pdb=" N   GLY H 104 "
        pdb=" CA  GLY H 104 "
        pdb=" C   GLY H 104 "
      ideal   model   delta    sigma   weight residual
     113.18  119.73   -6.55 2.37e+00 1.78e-01 7.65e+00
  ... (remaining 18554 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.53: 5057
       28.53 -    57.06: 1729
       57.06 -    85.59: 154
       85.59 -   114.12: 1
      114.12 -   142.65: 3
  Dihedral angle restraints: 6944
    sinusoidal: 4763
      harmonic: 2181
  Sorted by residual:
  dihedral pdb=" CA  LEU A  48 "
           pdb=" C   LEU A  48 "
           pdb=" N   ARG A  49 "
           pdb=" CA  ARG A  49 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.15   21.85     0      5.00e+00 4.00e-02 1.91e+01
  dihedral pdb=" C4'  DT J  15 "
           pdb=" C3'  DT J  15 "
           pdb=" O3'  DT J  15 "
           pdb=" P    DC J  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   77.35  142.65     1      3.50e+01 8.16e-04 1.41e+01
  dihedral pdb=" C4'  DG K  82 "
           pdb=" C3'  DG K  82 "
           pdb=" O3'  DG K  82 "
           pdb=" P    DT K  83 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   77.96  142.04     1      3.50e+01 8.16e-04 1.40e+01
  ... (remaining 6941 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 1919
       0.059 -    0.117: 182
       0.117 -    0.176: 9
       0.176 -    0.235: 1
       0.235 -    0.294: 2
  Chirality restraints: 2113
  Sorted by residual:
  chirality pdb=" CA  ILE B  29 "
            pdb=" N   ILE B  29 "
            pdb=" C   ILE B  29 "
            pdb=" CB  ILE B  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.73   -0.29 2.00e-01 2.50e+01 2.16e+00
  chirality pdb=" CG  LEU D 101 "
            pdb=" CB  LEU D 101 "
            pdb=" CD1 LEU D 101 "
            pdb=" CD2 LEU D 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.35   -0.24 2.00e-01 2.50e+01 1.46e+00
  chirality pdb=" CA  ILE A  62 "
            pdb=" N   ILE A  62 "
            pdb=" C   ILE A  62 "
            pdb=" CB  ILE A  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.20e+00
  ... (remaining 2110 not shown)

  Planarity restraints: 1328
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A  58 "   -0.012 2.00e-02 2.50e+03   2.31e-02 5.32e+00
        pdb=" C   THR A  58 "    0.040 2.00e-02 2.50e+03
        pdb=" O   THR A  58 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   GLU A  59 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU F  63 "   -0.010 2.00e-02 2.50e+03   2.00e-02 4.00e+00
        pdb=" C   GLU F  63 "    0.035 2.00e-02 2.50e+03
        pdb=" O   GLU F  63 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ASN F  64 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS F  59 "   -0.010 2.00e-02 2.50e+03   1.95e-02 3.78e+00
        pdb=" C   LYS F  59 "    0.034 2.00e-02 2.50e+03
        pdb=" O   LYS F  59 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   VAL F  60 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1325 not shown)

  Histogram of nonbonded interaction distances:
        2.55 -     3.02: 5941
        3.02 -     3.49: 11497
        3.49 -     3.96: 24618
        3.96 -     4.43: 27483
        4.43 -     4.90: 35706
  Nonbonded interactions: 105245
  Sorted by model distance:
  nonbonded pdb=" O5'  DA I 124 "
            pdb=" O4'  DA I 124 "
     model   vdw
     2.551 2.432
  nonbonded pdb=" N   ILE C  79 "
            pdb=" O   ILE C  79 "
     model   vdw
     2.586 2.496
  nonbonded pdb=" N   ILE G  79 "
            pdb=" O   ILE G  79 "
     model   vdw
     2.595 2.496
  nonbonded pdb=" N1   DG K 120 "
            pdb=" C4   DG K 120 "
     model   vdw
     2.595 2.672
  nonbonded pdb=" N1   DG J  67 "
            pdb=" C4   DG J  67 "
     model   vdw
     2.595 2.672
  ... (remaining 105240 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 11 through 117)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 34 through 124)
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.290
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     13.400
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8848
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12810  Z= 0.177
  Angle     :  0.602   9.236  18559  Z= 0.364
  Chirality :  0.037   0.294   2113
  Planarity :  0.005   0.043   1328
  Dihedral  : 28.410 142.653   5538
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  : 21.28 %
    Favored  : 78.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.53 (0.30), residues: 737
  helix:  1.62 (0.22), residues: 540
  sheet:  None (None), residues: 0
  loop : -0.61 (0.39), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E  42 
 TYR   0.012   0.001   TYR D  40 
 PHE   0.008   0.002   PHE C  25 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 (12810)
  covalent geometry    : angle       0.60230 (18559)
  hydrogen bonds       : bond        0.10508 (  778)
  hydrogen bonds       : angle       4.35954 ( 1934)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 162
  time to evaluate  : 0.337 
Fit side-chains
REVERT: D   86 ARG cc_start: 0.9257 (mmt90) cc_final: 0.9051 (mmt90)
REVERT: D  108 LYS cc_start: 0.9061 (mtpp) cc_final: 0.8682 (mtmp)
REVERT: D  116 LYS cc_start: 0.9266 (ttmm) cc_final: 0.9047 (ttmt)
REVERT: G   73 ASN cc_start: 0.8705 (t0) cc_final: 0.8161 (t160)
REVERT: G   91 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8719 (pm20)
  outliers start: 1
  outliers final: 1
  residues processed: 163
  average time/residue: 0.9281
  time to fit residues: 159.4238
Evaluate side-chains
  154 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 153
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.1980
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  85 GLN
G  68 ASN
G 104 GLN
H  63 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.103813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.074855 restraints weight = 19537.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.3109 rms_B_bonded: 1.26
r_work: 0.2896 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2745 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8845
moved from start:          0.0448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  12810  Z= 0.166
  Angle     :  0.556   8.404  18559  Z= 0.338
  Chirality :  0.034   0.213   2113
  Planarity :  0.004   0.039   1328
  Dihedral  : 30.533 142.962   4051
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 20.32 %
    Favored  : 78.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.20 (0.30), residues: 737
  helix:  2.12 (0.22), residues: 550
  sheet:  None (None), residues: 0
  loop : -0.55 (0.40), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  42 
 TYR   0.009   0.001   TYR D  40 
 PHE   0.013   0.002   PHE A  67 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (12810)
  covalent geometry    : angle       0.55589 (18559)
  hydrogen bonds       : bond        0.04081 (  778)
  hydrogen bonds       : angle       3.34272 ( 1934)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 158
  time to evaluate  : 0.338 
Fit side-chains
REVERT: D   71 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7868 (mp0)
REVERT: G   73 ASN cc_start: 0.8691 (t0) cc_final: 0.8146 (t160)
  outliers start: 9
  outliers final: 2
  residues processed: 162
  average time/residue: 0.9404
  time to fit residues: 160.3993
Evaluate side-chains
  161 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 158
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 HIS
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain D residue   71 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 54 optimal weight:    4.9990
   chunk 43 optimal weight:    4.9990
   chunk 42 optimal weight:    0.8980
   chunk 1 optimal weight:    3.9990
   chunk 9 optimal weight:    4.9990
   chunk 18 optimal weight:    3.9990
   chunk 83 optimal weight:    4.9990
   chunk 85 optimal weight:   10.0000
   chunk 46 optimal weight:    1.9990
   chunk 91 optimal weight:    4.9990
   overall best weight:    3.1788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
G 104 GLN
H  63 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.100085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.071427 restraints weight = 19869.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.2978 rms_B_bonded: 1.26
r_work: 0.2763 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2608 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8876
moved from start:          0.1297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.060  12810  Z= 0.345
  Angle     :  0.617   7.271  18559  Z= 0.369
  Chirality :  0.040   0.210   2113
  Planarity :  0.005   0.047   1328
  Dihedral  : 31.197 149.104   4051
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 18.08 %
    Favored  : 79.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.23 (0.30), residues: 737
  helix:  2.26 (0.22), residues: 538
  sheet:  None (None), residues: 0
  loop : -0.74 (0.38), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  35 
 TYR   0.014   0.002   TYR A  54 
 PHE   0.014   0.002   PHE A  67 
 HIS   0.004   0.001   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00791 (12810)
  covalent geometry    : angle       0.61708 (18559)
  hydrogen bonds       : bond        0.05017 (  778)
  hydrogen bonds       : angle       3.10015 ( 1934)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 150
  time to evaluate  : 0.312 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8671 (pm20) cc_final: 0.8404 (pm20)
REVERT: C   75 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8895 (mmtm)
REVERT: D   71 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7970 (mp0)
REVERT: F   92 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8486 (ttp80)
REVERT: G   73 ASN cc_start: 0.8897 (t0) cc_final: 0.8278 (t0)
  outliers start: 17
  outliers final: 6
  residues processed: 160
  average time/residue: 0.9740
  time to fit residues: 163.8359
Evaluate side-chains
  160 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 151
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 HIS
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain C residue   75 LYS
Chi-restraints excluded: chain C residue   95 LYS
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   95 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 53 optimal weight:    0.6980
   chunk 7 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 82 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 44 optimal weight:    0.6980
   chunk 84 optimal weight:    5.9990
   chunk 87 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** C  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN
H  63 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.101621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.072526 restraints weight = 19571.937|
|-----------------------------------------------------------------------------|
r_work (start): 0.3021 rms_B_bonded: 1.27
r_work: 0.2807 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2652 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8854
moved from start:          0.1224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12810  Z= 0.160
  Angle     :  0.566   8.416  18559  Z= 0.343
  Chirality :  0.035   0.274   2113
  Planarity :  0.004   0.044   1328
  Dihedral  : 31.164 148.253   4051
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 18.56 %
    Favored  : 78.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.49 (0.30), residues: 737
  helix:  2.41 (0.22), residues: 538
  sheet:  None (None), residues: 0
  loop : -0.52 (0.39), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  86 
 TYR   0.013   0.001   TYR F  51 
 PHE   0.010   0.001   PHE A  67 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (12810)
  covalent geometry    : angle       0.56621 (18559)
  hydrogen bonds       : bond        0.03818 (  778)
  hydrogen bonds       : angle       2.99757 ( 1934)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 157
  time to evaluate  : 0.315 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8619 (pm20) cc_final: 0.8394 (pm20)
REVERT: B   79 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8977 (mtpp)
REVERT: C   75 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8983 (mmtm)
REVERT: D   71 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7980 (mp0)
REVERT: F   92 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8498 (ttp80)
REVERT: G   73 ASN cc_start: 0.8846 (t0) cc_final: 0.8204 (t0)
  outliers start: 17
  outliers final: 5
  residues processed: 166
  average time/residue: 0.9748
  time to fit residues: 170.1571
Evaluate side-chains
  162 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 153
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain C residue   75 LYS
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   95 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 87 optimal weight:    7.9990
   chunk 4 optimal weight:    4.9990
   chunk 75 optimal weight:    5.9990
   chunk 91 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 98 optimal weight:    6.9990
   chunk 32 optimal weight:    5.9990
   chunk 39 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.9582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
G 104 GLN
H  63 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.103223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.074211 restraints weight = 19649.649|
|-----------------------------------------------------------------------------|
r_work (start): 0.3097 rms_B_bonded: 1.27
r_work: 0.2887 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2737 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8856
moved from start:          0.1231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  12810  Z= 0.170
  Angle     :  0.544   6.755  18559  Z= 0.331
  Chirality :  0.033   0.219   2113
  Planarity :  0.004   0.043   1328
  Dihedral  : 30.752 144.021   4049
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 19.68 %
    Favored  : 78.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.78 (0.30), residues: 737
  helix:  2.64 (0.22), residues: 538
  sheet:  None (None), residues: 0
  loop : -0.48 (0.39), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  86 
 TYR   0.009   0.001   TYR D  40 
 PHE   0.011   0.001   PHE A  67 
 HIS   0.002   0.001   HIS H  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 (12810)
  covalent geometry    : angle       0.54417 (18559)
  hydrogen bonds       : bond        0.03372 (  778)
  hydrogen bonds       : angle       2.83957 ( 1934)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 159
  time to evaluate  : 0.302 
Fit side-chains
REVERT: C   75 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8989 (mmtm)
REVERT: D   71 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7872 (mp0)
REVERT: F   92 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8481 (ttp80)
REVERT: G   73 ASN cc_start: 0.8789 (t0) cc_final: 0.8194 (t160)
  outliers start: 10
  outliers final: 3
  residues processed: 164
  average time/residue: 0.9769
  time to fit residues: 168.3496
Evaluate side-chains
  159 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 153
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain C residue   75 LYS
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   92 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 74 optimal weight:    5.9990
   chunk 66 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 36 optimal weight:    5.9990
   chunk 77 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    1.2984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
C 104 GLN
G 104 GLN
H  63 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.102608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.073500 restraints weight = 19589.596|
|-----------------------------------------------------------------------------|
r_work (start): 0.3081 rms_B_bonded: 1.26
r_work: 0.2869 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2719 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8867
moved from start:          0.1261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12810  Z= 0.191
  Angle     :  0.560  10.088  18559  Z= 0.336
  Chirality :  0.034   0.258   2113
  Planarity :  0.004   0.043   1328
  Dihedral  : 30.793 144.542   4049
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 19.68 %
    Favored  : 77.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.84 (0.30), residues: 737
  helix:  2.68 (0.22), residues: 538
  sheet:  None (None), residues: 0
  loop : -0.42 (0.39), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  86 
 TYR   0.010   0.001   TYR B  51 
 PHE   0.011   0.002   PHE A  67 
 HIS   0.003   0.001   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 (12810)
  covalent geometry    : angle       0.55968 (18559)
  hydrogen bonds       : bond        0.03604 (  778)
  hydrogen bonds       : angle       2.84004 ( 1934)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 154
  time to evaluate  : 0.312 
Fit side-chains
REVERT: D   71 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7917 (mp0)
REVERT: F   92 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8506 (ttp80)
REVERT: G   56 GLU cc_start: 0.9197 (OUTLIER) cc_final: 0.8914 (tt0)
REVERT: G   73 ASN cc_start: 0.8818 (t0) cc_final: 0.8230 (t160)
  outliers start: 15
  outliers final: 5
  residues processed: 162
  average time/residue: 0.9712
  time to fit residues: 165.4090
Evaluate side-chains
  161 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 153
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   95 LYS
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   56 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0970
   chunk 17 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   chunk 68 optimal weight:    0.3980
   chunk 50 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
G 104 GLN
H  63 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.102921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.073910 restraints weight = 19499.275|
|-----------------------------------------------------------------------------|
r_work (start): 0.3091 rms_B_bonded: 1.26
r_work: 0.2878 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2727 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.2727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8861
moved from start:          0.1290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  12810  Z= 0.169
  Angle     :  0.563  11.198  18559  Z= 0.336
  Chirality :  0.034   0.299   2113
  Planarity :  0.004   0.044   1328
  Dihedral  : 30.797 144.575   4049
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 21.76 %
    Favored  : 76.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.90 (0.30), residues: 737
  helix:  2.72 (0.22), residues: 538
  sheet:  None (None), residues: 0
  loop : -0.40 (0.39), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  86 
 TYR   0.009   0.001   TYR B  51 
 PHE   0.011   0.001   PHE A  67 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 (12810)
  covalent geometry    : angle       0.56277 (18559)
  hydrogen bonds       : bond        0.03498 (  778)
  hydrogen bonds       : angle       2.83626 ( 1934)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 153
  time to evaluate  : 0.326 
Fit side-chains
REVERT: D   71 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7913 (mp0)
REVERT: F   92 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8276 (ttp80)
REVERT: G   56 GLU cc_start: 0.9194 (OUTLIER) cc_final: 0.8908 (tt0)
REVERT: G   73 ASN cc_start: 0.8808 (t0) cc_final: 0.8217 (t160)
  outliers start: 9
  outliers final: 4
  residues processed: 159
  average time/residue: 0.9489
  time to fit residues: 158.6544
Evaluate side-chains
  159 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 152
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain G residue   56 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 96 optimal weight:    4.9990
   chunk 54 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 99 optimal weight:    7.9990
   chunk 68 optimal weight:    0.0980
   chunk 75 optimal weight:    4.9990
   chunk 97 optimal weight:    4.9990
   chunk 80 optimal weight:    3.9990
   chunk 89 optimal weight:    3.9990
   chunk 92 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    2.6188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
F  75 HIS
G 104 GLN
H  63 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.100778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.072193 restraints weight = 19507.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.2995 rms_B_bonded: 1.24
r_work: 0.2781 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2627 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8846
moved from start:          0.1418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.051  12810  Z= 0.301
  Angle     :  0.610  11.790  18559  Z= 0.360
  Chirality :  0.038   0.264   2113
  Planarity :  0.004   0.047   1328
  Dihedral  : 30.970 147.582   4049
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 20.64 %
    Favored  : 76.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.61 (0.30), residues: 737
  helix:  2.54 (0.22), residues: 538
  sheet:  None (None), residues: 0
  loop : -0.60 (0.38), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  86 
 TYR   0.013   0.002   TYR B  51 
 PHE   0.011   0.002   PHE D  70 
 HIS   0.004   0.001   HIS D  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00691 (12810)
  covalent geometry    : angle       0.60975 (18559)
  hydrogen bonds       : bond        0.04847 (  778)
  hydrogen bonds       : angle       2.96641 ( 1934)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 150
  time to evaluate  : 0.335 
Fit side-chains
REVERT: B   79 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8992 (mtpp)
REVERT: D   71 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7956 (mp0)
REVERT: F   92 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.8505 (ttp80)
REVERT: G   73 ASN cc_start: 0.8897 (t0) cc_final: 0.8281 (t0)
  outliers start: 15
  outliers final: 4
  residues processed: 157
  average time/residue: 0.9682
  time to fit residues: 159.5464
Evaluate side-chains
  157 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 150
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   92 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 83 optimal weight:    4.9990
   chunk 31 optimal weight:    0.8980
   chunk 96 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9980
   chunk 54 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   chunk 13 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
G 104 GLN
H  63 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.101499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.072498 restraints weight = 19379.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.3062 rms_B_bonded: 1.26
r_work: 0.2844 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2691 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8886
moved from start:          0.1396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12810  Z= 0.174
  Angle     :  0.589  11.571  18559  Z= 0.349
  Chirality :  0.035   0.330   2113
  Planarity :  0.004   0.049   1328
  Dihedral  : 31.022 147.744   4049
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 21.44 %
    Favored  : 76.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.67 (0.30), residues: 737
  helix:  2.57 (0.22), residues: 538
  sheet:  None (None), residues: 0
  loop : -0.53 (0.39), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  86 
 TYR   0.011   0.001   TYR B  51 
 PHE   0.010   0.001   PHE A  67 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 (12810)
  covalent geometry    : angle       0.58856 (18559)
  hydrogen bonds       : bond        0.04136 (  778)
  hydrogen bonds       : angle       2.93707 ( 1934)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 155
  time to evaluate  : 0.240 
Fit side-chains
REVERT: B   79 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.9034 (mtpp)
REVERT: D   71 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7981 (mp0)
REVERT: F   92 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8239 (ttp80)
REVERT: G   73 ASN cc_start: 0.8860 (t0) cc_final: 0.8257 (t0)
  outliers start: 10
  outliers final: 4
  residues processed: 160
  average time/residue: 0.9786
  time to fit residues: 164.3662
Evaluate side-chains
  162 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 155
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   92 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 69 optimal weight:    0.9980
   chunk 92 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 18 optimal weight:    4.9990
   chunk 72 optimal weight:    8.9990
   chunk 30 optimal weight:    0.9990
   chunk 89 optimal weight:    4.9990
   chunk 59 optimal weight:    3.9990
   chunk 41 optimal weight:    0.8980
   overall best weight:    0.8782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
G 104 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.102273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.073822 restraints weight = 19530.841|
|-----------------------------------------------------------------------------|
r_work (start): 0.3070 rms_B_bonded: 1.22
r_work: 0.2858 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2707 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8858
moved from start:          0.1409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12810  Z= 0.178
  Angle     :  0.585  11.080  18559  Z= 0.347
  Chirality :  0.034   0.283   2113
  Planarity :  0.004   0.047   1328
  Dihedral  : 30.972 146.831   4049
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 22.08 %
    Favored  : 76.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.75 (0.30), residues: 737
  helix:  2.63 (0.22), residues: 538
  sheet:  None (None), residues: 0
  loop : -0.51 (0.39), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  86 
 TYR   0.010   0.001   TYR B  51 
 PHE   0.011   0.001   PHE A  67 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 (12810)
  covalent geometry    : angle       0.58480 (18559)
  hydrogen bonds       : bond        0.03791 (  778)
  hydrogen bonds       : angle       2.91095 ( 1934)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1474 Ramachandran restraints generated.
    737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 155
  time to evaluate  : 0.320 
Fit side-chains
REVERT: B   79 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.9017 (mtpp)
REVERT: D   71 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7966 (mp0)
REVERT: F   92 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8522 (ttp80)
REVERT: G   73 ASN cc_start: 0.8857 (t0) cc_final: 0.8248 (t0)
  outliers start: 8
  outliers final: 4
  residues processed: 159
  average time/residue: 0.9865
  time to fit residues: 164.7119
Evaluate side-chains
  161 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 154
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   92 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 75 optimal weight:    5.9990
   chunk 51 optimal weight:    0.5980
   chunk 63 optimal weight:    3.9990
   chunk 78 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 26 optimal weight:    0.0570
   chunk 53 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.8902

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
G 104 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.102412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.073976 restraints weight = 19549.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.3071 rms_B_bonded: 1.22
r_work: 0.2861 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2710 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8859
moved from start:          0.1401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12810  Z= 0.171
  Angle     :  0.579  11.066  18559  Z= 0.344
  Chirality :  0.034   0.293   2113
  Planarity :  0.004   0.048   1328
  Dihedral  : 30.965 146.697   4049
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 21.76 %
    Favored  : 76.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.76 (0.30), residues: 737
  helix:  2.63 (0.22), residues: 538
  sheet:  None (None), residues: 0
  loop : -0.49 (0.39), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  86 
 TYR   0.010   0.001   TYR B  51 
 PHE   0.011   0.001   PHE A  67 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 (12810)
  covalent geometry    : angle       0.57948 (18559)
  hydrogen bonds       : bond        0.03726 (  778)
  hydrogen bonds       : angle       2.90542 ( 1934)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4770.39 seconds
wall clock time: 81 minutes 36.46 seconds (4896.46 seconds total)